|
| Status |
Public on Dec 31, 2021 |
| Title |
Sorghum leaves-control degradome |
| Sample type |
SRA |
| |
|
| Source name |
Sorghum leaves
|
| Organism |
Sorghum bicolor |
| Characteristics |
tissue: leaves
treatment: control
|
| Treatment protocol |
To impose heat stress, 30 days after sowing, sorghum seedlings grown at 28°/20°C (day/night) were transferred to another growth chamber maintained at 38°/30°C (day/night) for 50 days. Drought stress was imposed by withholding irrigation for one week on 73-day-old (after sowing) plants grown at 28°/20°C (day/night). Drought and heat combination was imposed by withholding irrigation for one week on 73-day-old (after sowing) plants grown at 38°/30°C (day/night). At the end of stress treatment, leaf samples from control, drought or heat, drought and heat-stressed plants were harvested
|
| Growth protocol |
Sorghum (Sorghum bicolor (L.) Moench) seeds were sown in pots (0.2 m diameter × 0.45 m tall) filled with pure, fine sand soil and grown in growth chambers (Conviron Ltd., Winnipeg, Canada) at 28°/20°C (day/night) with a photoperiod of 14 h/10 h (day/night). After germination, sorghum seedlings were thinned to one plant per pot.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from leaves of control, drought or heat, drought and heat-exposed sorghum using the Trizol reagent
Degradome libraries were constructed using poly-A+ RNA, which was ligated to a 5’adapter containing a MmeI site at its 3’-end. The ligated products were used for cDNA production and amplified by PCR for five cycles. The PCR products were digested with MmeI and the resulting fragments ligated to a second double-stranded oligonucleotide, purified and amplified for another ten PCR cycles. The PCR product has been purified and sequenced.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Cut the first 20 nucleotides in the remaining reads
Sort and remove repetitive sequences
Calculate the counts of unique sequences
Supplementary_files_format_and_content: sequences and count values
|
| |
|
| Submission date |
Sep 04, 2020 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Yun Zheng |
| E-mail(s) |
zhengyun5488@gmail.com
|
| Organization name |
Yunnan Agricultural University
|
| Street address |
452 Fengyuan Road
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650201 |
| Country |
China |
| |
|
| Platform ID |
GPL21615 |
| Series (1) |
| GSE157521 |
Degradome profiles in leaves of Sorghum exposed to drought or heat or their combination |
|
| Relations |
| BioSample |
SAMN16063235 |
| SRA |
SRX9078302 |
